[gmx-users] Problem with pdb2gmx when used with OPLS and TIP4P

Manik Mayur manik.mayur at gmail.com
Wed May 13 21:50:53 CEST 2009

Hi Users,

I constructed a .pdb file for TIP4P water model which I tried to convert to
.gro using pdb2gmx using:

$ pdb2gmx -f Sim1.pdb -o Sim1.gro -water tip4p

with the choice of forcefield as 5 (OPLS-AA/L all-atom force field). After
conversion I found that the position of HW3(MW), the dummy atom is not the
same relative to OW, what I kept in the .pdb file. Even during the
conversion pdb2gmx gave warnings as "Warning: Long Bond (1773-1776 =....".
My .pdb file goes like this:
ATOM   1773  OW  SOL   108      45.944  29.409  58.762  1.00  0.00
ATOM   1774  HW1 SOL   108      46.530  29.409  59.519  1.00  0.00
ATOM   1775  HW2 SOL   108      46.530  29.409  58.005  1.00  0.00
ATOM   1776  HW3  SOL   108      46.094  29.409  58.762  1.00  0.00
note that the OW - HW3 is 0.15 angs as it should be.

So why is pdb2gmx recalculating the co-ordinates of HW3? How is the OW-HW3
bond is getting stretched? Also, what should be the correct procedure for
the conversion?


Manik Mayur
Graduate student
Microfluidics Lab
Dept. of Mechanical Engg.
IIT Kharagpur
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